On 12/2/2019 7:12 PM, Joëlle Ismay Rosanne Van Der Molen wrote:
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Dear Freesurfer experts,
After running the -qcache option to extract thickness data for every subject, I
tried pulling all the data together in order to get a matrix of subjects x
vertices containing thickness data (for a given hemisphere) in all vertices of
the brain.
I noticed that for some small areas, particularly medial temporal, thickness
data equals to 0 for some subjects, and has values for other subjects. May this
be of concern? If so, would you have any idea why this is happening?
It is hard to say without seeing the locations. There are sometimes places on
the edge of the medial wall where there are some small errors in registration
and so things don't line up perfectly. Could that be it?
Another, perhaps related question is: when I try to use a subject's individual
thickness mgh as an overlay in tksurfer, I obtain the outputs attached to this
email (I am not modifying any overlay min max or threshold values). I am
wondering if these grey zones in the map (around occipital and parietal areas
specifically; not for subcortical areas) are to be expected, or if they may
reflect some processing problem? If so, what problem could it be?
I would say that those images look problematic. Is that the individual's
surface or is it after mapping to fsaverage? In any event, you should look at
the surfaces overlaid on the volume to see if the thickness is 0.
Thank you in advance for your help,
Best regards,
Joëlle van der Molen
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